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  • Estimation of genome size from Nanopore using jellyfish

    Hi,
    I would like to calculate the genome size from the whole genome ONT nanopore reads (~8.7 GB) for a plant genome. My aim is to assemble the mitochondrial genome from ONT nanopore reads. I knew the approximate chloroplast genome size (165kb) and the mitochondrial genome is ~1 MB. But I do not know the depth coverage and expected genome size. I am very beginner and don't know how to calculate both depth coverage and genome size. I have used jellyfish and 27 kmer length to calculate the genome size but not able to get a good result.
    input parameter:
    ./jellyfish count -m 27 -s 100M -t 10 -C ONT.fastq

    Please help me to find out the expected genome size.
    Thank you.

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  • #2
    Very likely the ONT data are not suitable for the kmer analysis. The read error rate is likely too high. Every 27 nt stretch can be expected to contain errors?

    This will work with Illumina or HiFi data.

    Comment

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